def test_open_structure(self):
param = {}
param['structure_phase_0'] = 'oPPA.cif'
# param['structure_datablock'] = 'oPPA'
structure = reflections.open_structure(param,0)
self.assertEqual(param['sgno_phase_0'],4)
self.assertEqual([8.5312,4.8321,10.125,90.00,92.031,90.00],
param['unit_cell_phase_0'])
def test_calc_intensity(self):
myinput = check_input.parse_input(input_file='simul.inp')
myinput.read()
myinput.check()
myinput.initialize()
myinput.param['structure_phase_0'] = 'oPPA.cif'
myinput.param['structure_datablock'] = 'oPPA'
xtal_structure = reflections.open_structure(myinput.param,0)
hkl = reflections.gen_miller(myinput.param,0)
hkl = reflections.calc_intensity(hkl,xtal_structure)
def intensity(inp):
"""
Reject peaks based on intensity
Jette Oddershede, August 27 2008
Absorption correction added December 2011
"""
if inp.files['structure_file'] != None:
inp.param['structure_phase_0'] = inp.files['structure_file']
xtal_structure = reflections.open_structure(inp.param,0)
hkl = reflections.gen_miller(inp.param,0)
hkl = reflections.calc_intensity(hkl,xtal_structure)
# print hkl
if inp.fit['abs_mu'] > 0:
xmin = min(inp.fit['abs_xlim'])*1e3
xmax = max(inp.fit['abs_xlim'])*1e3
ymin = min(inp.fit['abs_ylim'])*1e3
ymax = max(inp.fit['abs_ylim'])*1e3
for i in range(inp.no_grains):
x = deepcopy(inp.values['x%s' %i])
y = deepcopy(inp.values['y%s' %i])
z = deepcopy(inp.values['z%s' %i])
#Make sure that grain not outside of bounds for doing the correction
if inp.fit['abs_mu'] > 0:
if x < xmin:
x = xmin
elif x > xmax:
x = xmax
if y < ymin:
y = ymin
elif y > ymax:
y = ymax
for j in range(inp.nrefl[i]):
h = inp.h[i][j]
k = inp.k[i][j]
l = inp.l[i][j]
# Absorption correction start
if inp.fit['abs_mu'] > 0:
w = inp.w[inp.id[i][j]]
dety = inp.dety[inp.id[i][j]]
detz = inp.detz[inp.id[i][j]]
Omega = tools.form_omega_mat_general(w*n.pi/180.,inp.values['wx']*n.pi/180.,inp.values['wy']*n.pi/180.)
R = tools.detect_tilt(inp.values['tx'],inp.values['ty'],inp.values['tz'])
d_out = n.dot(R,n.array([[0],
[(dety-inp.values['cy'])*inp.values['py']],
[(detz-inp.values['cz'])*inp.values['pz']]]))
d_out = d_out + n.array([[inp.values['L']],[0],[0]]) - n.dot(Omega,n.array([[x],[y],[z]]))
d_out = n.dot(n.transpose(Omega),d_out/n.sqrt(n.sum(d_out**2)))
d_in = n.dot(n.transpose(Omega),n.array([[-1],[0],[0]])) #from grain to source!
# distance to bounding planes assuming d_in and d_out unit vectors
xdist_in = 1e6
xdist_out = 1e6
ydist_in = 1e6
ydist_out = 1e6
if d_in[0] < 0:
xdist_in = (x-xmin)/abs(d_in[0,0])
elif d_in[0] > 0:
xdist_in = (xmax-x)/abs(d_in[0,0])
if d_in[1] < 0:
ydist_in = (y-ymin)/abs(d_in[1,0])
elif d_in[1] > 0:
ydist_in = (ymax-y)/abs(d_in[1,0])
dist_in = min(xdist_in,ydist_in)
if d_out[0] < 0:
xdist_out = (x-xmin)/abs(d_out[0,0])
elif d_out[0] > 0:
xdist_out = (xmax-x)/abs(d_out[0,0])
if d_out[1] < 0:
ydist_out = (y-ymin)/abs(d_out[1,0])
elif d_out[1] > 0:
ydist_out = (ymax-y)/abs(d_out[1,0])
dist_out = min(xdist_out,ydist_out)
dist = dist_in + dist_out
# abs_mu in mm-1 and dist in microns
exponential = n.exp(inp.fit['abs_mu']*dist*1e-3)
#print h,k,l,w,x,y,z,dist_in*1e-3,dist_out*1e-3,dist*1e-3,exponential
else:
exponential = 1.
# Absorption correction end
value = False
for m in range(len(hkl)):
if hkl[m][0] == h and hkl[m][1] == k and hkl[m][2] == l:
inp.volume[i][j] = inp.F2vol[inp.id[i][j]]/hkl[m][3]*exponential
value = True
break
else:
pass
if value == False:
# print i+1,j+1,h,k,l,'should never go here, ask osho for help...'
inp.volume[i][j] = -1
data = deepcopy(inp.volume)
minvol = []
maxvol = []
for i in range(inp.no_grains):
if i+1 in inp.fit['skip']:
pass
else:
rej = []
newreject = 1
while newreject > 0:
tmp = len(rej)
mad(data[i],rej,inp.fit['rej_vol'])
newreject = len(rej) - tmp
avgdata = n.sum(data[i])/len(data[i])
sigdata = spread(data[i])
if len(rej) > 1:
avgrej = n.sum(rej)/len(rej)
sigrej = spread(rej)
elif len(rej) == 1:
avgrej = rej[0]
sigrej = 0
else:
avgrej = 0
sigrej = 0
if len(data[i]) > 0:
minvol.append(max(0,min(data[i])))
maxvol.append(max(data[i]))
else:
minvol.append(0)
maxvol.append(-1)
if i+1 not in inp.fit['skip']:
inp.fit['skip'].append(i+1)
# print '\n',i, avgdata, sigdata, len(data[i]), minvol[i], maxvol[i],'\n ',avgrej, sigrej, len(reject)#,'\n',data[i],'\n',reject
delete = 0
for i in range(inp.no_grains):
if i+1 in inp.fit['skip']:
pass
else:
for j in range(inp.nrefl[i]-1,-1,-1):
if inp.volume[i][j] < minvol[i] or inp.volume[i][j] > maxvol[i]:
reject(inp,i,j,'intensity')
delete = delete + 1
print 'Rejected', delete, 'peaks because of different intensity scales'
insignificant(inp)
def intensity(inp):
"""
Reject peaks based on intensity
Jette Oddershede, August 27 2008
"""
if inp.files['structure_file'] != None:
inp.param['structure_phase_0'] = inp.files['structure_file']
xtal_structure = reflections.open_structure(inp.param, 0)
hkl = reflections.gen_miller(inp.param, 0)
hkl = reflections.calc_intensity(hkl, xtal_structure)
# print hkl
for i in range(inp.no_grains):
for j in range(inp.nrefl[i]):
h = inp.h[i][j]
k = inp.k[i][j]
l = inp.l[i][j]
value = False
for m in range(len(hkl)):
if hkl[m][0] == h and hkl[m][1] == k and hkl[m][2] == l:
inp.volume[i][j] = inp.F2vol[inp.id[i][j]] / hkl[m][3]
value = True
break
else:
pass
if value == False:
# print i+1,j+1,h,k,l,'should never go here, ask osho for help...'
inp.volume[i][j] = -1
data = deepcopy(inp.volume)
minvol = []
maxvol = []
for i in range(inp.no_grains):
if i + 1 in inp.fit['skip']:
pass
else:
rej = []
newreject = 1
while newreject > 0:
tmp = len(rej)
mad(data[i], rej, inp.fit['rej_vol'])
newreject = len(rej) - tmp
avgdata = n.sum(data[i]) / len(data[i])
sigdata = spread(data[i])
if len(rej) > 1:
avgrej = n.sum(rej) / len(rej)
sigrej = spread(rej)
elif len(rej) == 1:
avgrej = rej[0]
sigrej = 0
else:
avgrej = 0
sigrej = 0
if len(data[i]) > 0:
minvol.append(max(0, min(data[i])))
maxvol.append(max(data[i]))
else:
minvol.append(0)
maxvol.append(-1)
if i + 1 not in inp.fit['skip']:
inp.fit['skip'].append(i + 1)
# print '\n',i, avgdata, sigdata, len(data[i]), minvol[i], maxvol[i],'\n ',avgrej, sigrej, len(reject)#,'\n',data[i],'\n',reject
delete = 0
for i in range(inp.no_grains):
if i + 1 in inp.fit['skip']:
pass
else:
for j in range(inp.nrefl[i] - 1, -1, -1):
if inp.volume[i][j] < minvol[i] or inp.volume[i][
j] > maxvol[i]:
reject(inp, i, j, 'intensity')
delete = delete + 1
print('Rejected', delete,
'peaks because of different intensity scales')
insignificant(inp)
def find_refl(inp):
"""
From U, (x,y,z) and B determined for the far-field case
calculate the possible reflection on the near-field detector
output[grainno][reflno]=[h,k,l,omega,dety,detz,tth,eta]
"""
S = n.array([[1, 0, 0],[0, 1, 0],[0, 0, 1]])
R = tools.detect_tilt(inp.param['tilt_x'],
inp.param['tilt_y'],
inp.param['tilt_z'])
inp.possible = []
# if structure info is given use this
if inp.files['structure_file'] != None:
inp.param['structure_phase_0'] = inp.files['structure_file']
xtal_structure = reflections.open_structure(inp.param,0)
HKL = reflections.gen_miller(inp.param,0)
else:
inp.param['unit_cell_phase_0'] = inp.unit_cell
inp.param['sgno_phase_0'] = inp.fit['sgno']
HKL = reflections.gen_miller(inp.param,0)
for grainno in range(inp.no_grains):
inp.possible.append([])
if grainno+1 not in inp.fit['skip']:
B = tools.epsilon_to_b(n.array([inp.values['epsaa%s' %grainno],
inp.values['epsab%s' %grainno],
inp.values['epsac%s' %grainno],
inp.values['epsbb%s' %grainno],
inp.values['epsbc%s' %grainno],
inp.values['epscc%s' %grainno]]),
inp.unit_cell)
U = tools.rod_to_u([inp.rod[grainno][0]+inp.values['rodx%s' %grainno],
inp.rod[grainno][1]+inp.values['rody%s' %grainno],
inp.rod[grainno][2]+inp.values['rodz%s' %grainno]])
gr_pos = n.array([inp.values['x%s' %grainno],
inp.values['y%s' %grainno],
inp.values['z%s' %grainno]])
for hkl in HKL:
Gc = n.dot(B,hkl[0:3])
Gw = n.dot(S,n.dot(U,Gc))
tth = tools.tth2(Gw,inp.param['wavelength'])
# print hkl[0:3],tth*180./n.pi
costth = n.cos(tth)
(Omega, Eta) = tools.find_omega_general(inp.param['wavelength']/(4.*n.pi)*Gw,
tth,
inp.values['wx']*n.pi/180,
inp.values['wy']*n.pi/180)
if len(Omega) > 0:
for solution in range(len(Omega)):
omega = Omega[solution]
eta = Eta[solution]
for i in range(len(inp.fit['w_limit'])//2):
if (inp.fit['w_limit'][2*i]*n.pi/180) < omega and\
omega < (inp.fit['w_limit'][2*i+1]*n.pi/180):
# form Omega rotation matrix
Om = tools.form_omega_mat_general(omega,inp.values['wx']*n.pi/180,inp.values['wy']*n.pi/180)
Gt = n.dot(Om,Gw)
# Calc crystal position at present omega
[tx,ty,tz]= n.dot(Om,gr_pos)
# Calc detector coordinate for peak
(dety, detz) = detector.det_coor(Gt,costth,
inp.param['wavelength'],
inp.param['distance'],
inp.param['y_size'],
inp.param['z_size'],
inp.param['y_center'],
inp.param['z_center'],
R,tx,ty,tz)
#If peak within detector frame store it in possible
if (-0.5 < dety) and\
(dety < inp.fit['dety_size']-0.5) and\
(-0.5 < detz) and\
(detz < inp.fit['detz_size']-0.5):
inp.possible[grainno].append([hkl[0],
hkl[1],
hkl[2],
omega*180/n.pi,
dety,
detz,
tth,
eta])
def run(options):
# Check for print_input
try:
options.print_input
except:
options.print_input = None
if options.print_input:
print(help_input.show_input())
sys.exit()
# Check if filename is specified
try:
options.filename
except:
options.filename = None
if options.filename == None:
print("\nNo input file supplied [-i filename]\n")
#Gaelle comment : ? sys.exit() and add raise error instead
sys.exit()
#print 'options = ',options
#print '\n'
# Check killfile does not exist
try:
options.killfile
except:
options.killfile = None
if options.killfile is not None and os.path.exists(options.killfile):
print("The purpose of the killfile option is to create that file")
print("only when you want PolyXsim to stop")
print("If the file already exists when you start PolyXsim, it is")
print("stopped immediately")
raise ValueError("Your killfile " + options.killfile +
" already exists")
# Is the input file available?
# Read and check input
# Make instance of parse_input class
print('Reading input\n')
myinput = check_input.parse_input(input_file=options.filename)
myinput.read() # read input file
print('Checking input\n')
myinput.check() # check validity of input
check_input.interrupt(options.killfile)
# if myinput.missing == True: # if problem exit
# print('MISSING ITEMS')
# sys.exit()
if len(myinput.errors) > 0:
myinput.show_errors()
sys.exit()
print('Initialize parameters etc\n')
myinput.initialize() # if ok initialize
check_input.interrupt(options.killfile)
# Generate reflections
hkl = []
for phase in myinput.param['phase_list']:
if ('structure_phase_%i' % phase) in myinput.param:
xtal_structure = reflections.open_structure(myinput.param, phase)
#print 'UNIT CELL', myinput.param['unit_cell_phase_%i' %phase]
print('Generating miller indices')
hkl_tmp = reflections.gen_miller(myinput.param, phase)
if myinput.param['structure_factors'] != 0:
print('Structure factor calculation')
hkl.append(
reflections.calc_intensity(hkl_tmp, xtal_structure,
options.killfile))
else:
hkl.append(reflections.add_intensity(hkl, myinput.param))
print('No structure factor calculation')
else:
hkl_tmp = reflections.gen_miller(myinput.param, phase)
hkl.append(reflections.add_intensity(hkl_tmp, myinput.param))
check_input.interrupt(options.killfile)
# if options.killfile is not None and os.path.exists(options.killfile):
# raise KeyboardInterrupt()
generate_grains.generate_grains(myinput.param)
check_input.interrupt(options.killfile)
print('Write grains file')
file_io.write_grains(myinput.param)
check_input.interrupt(options.killfile)
print('Write res file')
file_io.write_res(myinput.param)
check_input.interrupt(options.killfile)
if '.hkl' in myinput.param['output']:
print('Write hkl file')
file_io.write_hkl(myinput.param, hkl)
if '.fcf' in myinput.param['output']:
print('Write fcf file')
file_io.write_fcf(myinput.param, hkl)
if '.ubi' in myinput.param['output']:
print('Write UBI file')
file_io.write_ubi(myinput.param)
if '.par' in myinput.param['output']:
print('Write detector.par file')
file_io.write_par(myinput.param)
check_input.interrupt(options.killfile)
# Determine the reflection parameters for grains
graindata = find_refl.find_refl(myinput.param, hkl, options.killfile)
graindata.frameinfo = myinput.frameinfo
print('Determine reflections positions')
graindata.run()
if '.ref' in myinput.param['output']:
print('Write reflection file')
graindata.save()
if '.gve' in myinput.param['output']:
print('Write g-vector file')
graindata.write_gve()
if '.ini' in myinput.param['output']:
print('Write GrainSpotter ini file - Remember it is just a template')
graindata.write_ini()
if '.flt' in myinput.param['output']:
print('Write filtered peaks file')
graindata.write_flt()
if myinput.param['make_image'] == 1:
if myinput.param['peakshape'][0] == 2:
image = make_imagestack.make_image(graindata, options.killfile)
image.setup_odf()
image.make_image_array()
image.make_image()
image.correct_image()
else:
image = make_image.make_image(graindata, options.killfile)
image.make_image()